The Color of Blood On Your Hands
by ShineBright
Summary: Weir recieves death threats from someone on Atlantis. Who is it? The staff's money's on John Sheppard.
1. Fighting

A/n I own nothing! No stargate! No Atlantis! Nothing! Absolutletly nothing! I'm a college student, what do you expect????

Chapter One

"I love you, Elizabeth," John whispered into her ear as he drew her in close.

The waves crashed against the building and sent sea-spray flying into the air. John and Elizabeth were safe, however, as they were on the top level of Atlantis with only the heavens above them, and only the future before them.

"I..." she stopped talking as footsteps approached. From a distance she could see it was Ford, Mckay, and Tayla. With out thinking she pushed the Major away.

He stumbled back, more from shock than her actual push.

"Elizabeth?" he asked bewilderedly.

"Yes, thank you, John that will be all," she said in an abnormally loud voice, "Now can you please stop pestering me?"

"Are you ok, Dr. Weir?" Ford asked as he stopped beside her eyeing Sheppard. Why was his CO hugging her?

"Yes, yes."

"_Well_ that's _good_ to hear. I'd like to continue this conversation later, too. I wasn't aware I was _pestering_ you. So sorry."

With that John stormed off, his angry footsteps echoed through the halls. Weir's guilt magnified the noise a hundred times greater till all she could hear was his thundering footsteps.

"What was he doing?"

"Um, nothing. _Nothing_. He just fell and I helped him up."

"Why did he fall?" McKay asked as he chewed on a granola bar.

"I think he was tired."

"Do we need to speak with him? He seems very angry."

"He's been preoccupied lately. Always sneaking around at night. It's not like him," Ford added to Mckay's assessment.

"Lieutenant, I haven't noticed anything amiss other than the lack of sleep. Why don't we just forget everything that happened? I think Major Sheppard has been under quite a bit of stress."

They all nodded, but no one believed her. Something was going on. And they were going to find out.

Later that night, Ford followed his CO as he made way to Weir's office.

_What is going on?_

Sheppard entered her office, and closed the door securely with a click of the lock. Ford pressed his ear against the door. He couldn't make out everything because the Ancients made the door too darn thick. Luckily for him they were shouting.

"How could you ...?"

"John, you are acting ...."

"So what did you tell them? That I lost...?"

"Goodness no! .... I told them you fell...."

"Oooh, great. ..."

"No...."

"... Wouldn't you entrust your life to me now? ... stressed freak ...?"

"John, you are taking this too far. ...."

"Oh? Really? ...NEVER SHOW WEAKNESS."

"It ...."

"... going back ...."

"No..."

"You said you were sick..."

"I can't..."

"Oh."

"I'm ...."

"No...."

"_John_."

"... Major Sheppard."

"I'm sorry. ..That I took advantage of my...my position ...? Would I ..."

"I was willing to take risks... couldn't step up to the plate."

"JOHN!"

"Major ..., please. Goodnight ....."

"No, no!..I ... I will!"

"No. It's ok."

"Please."

"Don't beg Doctor Weir. Goodnight."

"I ..."

"Don't you see? You humiliated me... I won't be used. I won't."

"But..."

"You're ... dead, Elizabeth."

Ford shivered, he had heard too much. The doorknob began to turn, and he ran to tell Mckay.

"How could you embarrass me in front of my men?"

"John, you are acting like a little school boy."

"So what did you tell them? That I lost a contact on your blouse?"

"Goodness no! You don't even wear contacts. I told them you fell."

"Oooh, great. I fell. On what? My own two freakin' feet?"

"No...because you were stressed and tired."

"Oh! Even better, Elizabeth. Wouldn't you entrust your life to me now? Some bumbling stressed freak who can't even stand?"

"John, you are taking this too far. I'm sure they've forgotten it by now."

"Oh? Really? I know my men. They won't forget. Rule number one Elizabeth for a person in military command-NEVER SHOW WEAKNESS."

"It applies to me too, you know. 'Specially as a woman."

"So you're going back on your promise."

"No...delay..."

"You said you were sick of hiding our relationship. I am too. So we're not going to announce it on..."

"I can't John."

"Oh."

"I'm sorry."

"No, you are ashamed."

"_John_."

"I'd prefer if you called me Major Sheppard."

"I'm sorry. I...If I tell everyone that I'm in love with you, how would that look? That I took advantage of my...my position as your boss? Would I loose respect?"

"I was willing to take risks, Doctor Weir, for us to work out. It would have been nice. But I'm not the type to beg. And you know that. I respect your decision. It is truly a regret that you just couldn't step up to the plate."

"JOHN!"

"Major Sheppard, please. Goodnight Elizabeth."

"No, no!" She grabbed his arm as he turned to leave, "I love you! I love you so much! I'll tell them, I will!"

He shook her hand off.

"No. It's ok."

"Please."

"Don't beg Doctor Weir. Goodnight."

"I love you!"

"Don't you see? You humiliated me, made my men doubt me and all from being ashamed to admitting in public you love me. I won't be used. I won't."

"But..."

"You're love to me is dead, Elizabeth."

With that he left.

Weir collapsed in her chair and buried her face in her hands.


	2. Questions

**Chapter 2**

McKay was floored when Ford told him about the fight between Sheppard and Weir. To him they always got along. They seemed to be good friends. Very good friends...It bothered him that his superior mind could not come up with an idea about what was going on between them.

Why was he hugging her? Mckay didn't buy into the Major falling on her. The man didn't have an ounce of clumsiness in him.

"Maybe they were making out, or something," Ford suggested.

But they laughed as if it was the most improbable explanation ever. Weir and Sheppard? Weren't they always at odds about missions and regulations? Their last fight even proved their distaste for each other.

"Do you think he was...ah...Now I don't want to say this, because I don't think it's true, Ford, but what if-what if he was making a move on her...and she denied him."

"That would explain the fight and why he was embarrassed."

"And why Weir would want to forget all this."

"And their fight."

They looked at each other and shook their heads.

"Nooo..."

But their hearts said yes.

McKay and Ford rapped lightly on John's door.

"Come in."

Timidly, they opened the door, but remained in the doorway. The Major put his book down and gestured for them to take a seat. He sat up on his bed and swung his legs around, ready for a conference.

But they stayed in the doorway.

"Sir..." Ford began timidly, "Are you and Doctor Weir...an, an...item?"

"No."

"What was going on up..."

"Nothing for you or anyone to know. I fell, like Doctor Weir said. Take it or leave it."

"We don't believe you."

John raised his eyebrow and stood up. He towered over them, not with his height, but with his forceful manner.

"Say it straight Ford. What do you want me to tell you?"

"Truth, sir," the Lieutenant said now standing at attention.

"Have you asked to speak freely?"

"No."

"Ask."

"May I speak freely, sir?"

"No."

"I'm a civilian. I'll ask. Did she reject you?"

The Major burrowed his eyebrows and grabbed the door, ready to slam it in their faces. But he withheld his emotions, as he was taught to do, and lessened his grip on the doorknob.

"I don't understand, McKay. There was nothing to reject."

"You hugged her."

"Do you want a hug, Mckay?"

"What?!"

"Are you jealous?"

"Major, I, most certainly..."

Before he could get the rest of his denial out, the Major swept him up in a hug and thumped on his back. The "man hug".

"Happy now?"

"Yes sir," Ford answered not wanting a hug.

"Goodnight then."

With that the Major shut his door softly, leaving Ford and Mckay in the hall. Bewildered.

"He's good, Rod."

"Huh?"

"He's the best at avoiding answering."

"I got hugged," Rodney shivered and then laughed, "You're right though. After that, I'm not asking any more questions. At least not him."

"Doctor Weir?"

She looked up from her desk and smiled, well, fake smiled, at Kavanah.

"Yes?"

"I have a question on some experiments I need to run."

He took a seat across from her and placed a shoe sized box on his lap.

"What is it?"

"Well, permission basically."

"What is the _experiment_?"

"It's really complicated to explain, and a long drawn out explanation in layman's terms would simplify it to the extent that the essence..."

"Simplify or you don't have permission."

He rolled his eyes and let out a huff, but ultimately she had the authority, and her eyebrow was raised. Even by now Kavanah knew not to miss with her when that thing shot up.

"The shield device Rodney had...What if it could generate enough power to protect the whole base in the event that our current shield was deactivated or hindered by an enemy projectile, or some energy stream."

"Back ups are always good, Kavanah, but how would you test it?"

"See...that's the hard part. Sheppard has the most potent Ancient gene. If we hooked him up to it, and replicated the connecter and also connected it to the power source of the base's shield, we may have a new ZPM type if you will..."

"Would this cause any damage to John...the Major."

"Well...no?"

The eyebrow shot up again.

"No."

Her eye squinted.

"Oh FINE! Yes! It'll probably kill him if he's hooked up too long, but if we do it right, then he may just loose consciousness."

"I'm sorry Kavanah. I can't give you permission."

"It's just because you're in love with him isn't it?"

She gasped and gripped at the table till her knuckles turned white. He smirked, and a glint of contempt shined in his eyes.

"Kavanah," she began slowly, "You are not to tell anyone what you just said."

"So it's true. I heard you two were hugging the other night."

Inwardly she groaned to herself. It never occurred to her to deny it again.

"He fell, it wasn't a hug. And I don't love him; see...Why am I even explaining myself to you? I'm busy, is that all you wanted to discuss?"

"Yeah. Sure."

Weir got up and closed the door behind him. Sighing, she tidied up her office and got ready to turn in for the day. She was in no condition to govern anything right now.

It was an hour later before Elizabeth could get to bed. On the way to her quarters she ran into Beckett who was excitedly chattering about some new band aid creation he found...or something like that. All Elizabeth remembered was that she snapped at him. Then Ford and Mckay came firing more questions, but she snapped at them too.

Tayla even asked if she was pregnant because of her mood swings, and the Athosian had just learned from someone that earth women experienced mood swings and fits of emotion when they were pregnant. Elizabeth had barked her head off for that comment...Probably not disproving the other woman's theory...

That would be handled later.

Curled up under her covers, she couldn't sleep. The day's events kept running though her mind.

_I can't believe I hurt him like that. I love you John! I'm so sorry._

It scared her that she might loose him. He always had tough exterior, but he had opened up to her, Elizabeth knew she was the only one on base who had penetrated that humorous bravado. And now that she rejected him...John put his hard military shell up...that cocky smile was still there...and so was the smirk...but now none of it would reflect in his eyes. It would be cold.

_I lost him._

Who was she kidding? She couldn't sleep.

"Might as well catch up on work."

And that's when she found it. Under her office door. A letter.


	3. Letters

a/n Thanks for all the reviews! I love getting mail! I'm updating this thing fast bc I have free time. What's that again? I've forgotten it's been so long...

**Chapter3**

Gingerly, Elizabeth picked it up and peeled the letter away from inside the envelope. As she unfolded it, red sequence fell away from the note.

_What on earth?_

(Or, um, what on Atlantis)

**Remember. I don't sleep at night.**

**Remember I don't sleep in the day.**

**Remember, you are always on my mind.**

**Remember as you sleep forever.**

_What?!_

A shiver ran up her spine as she locked herself in the office. At any other time she would have called John to come. As she sat in her chair she realized no one else would come rushing to her at this hour without complaining.

_What is this?? A threat? Sleep forever?_

Weir looked around her office and through her windows, she was utterly alone. The darkness smothered her view of everything beyond her desk.

_I should have stayed in my quarters._

But, she was street-wise enough to know that walking back to her room was not smart. It was probably just what the psycho would want. Was it a psycho? Maybe it was a Joke. A joke from John to make her laugh...But even he wasn't perverted like that. No one on base was.

All the sudden she began to feel tired again. The weight of the day fell on her like a ton of bricks and her eyes felt as if they were being held down as well. Fighting it, she sat up at her desk, ram-rod straight....watching for her "poet" as she forced her stinging eyes open.

And that was how McKay found her. At her desk, her head resting on it, on top of her letter and a pile of red sequence. The sequence had intertwined with her hair and stuck to her skin like burrs.

"Umm...Elizabeth?"

Her eyes jerked open and the world came into focus. Sitting up again, she smiled, but could not conceal her worries.

"Everything ok?"

"Yes, yes. I thought my door was locked."

He shrugged.

"Must not be working. Or maybe you forgot. Here," he slid an envelope across the table at her.

"I locked it."

"Okay..."

"Get someone to fix it immediately."

"Elizabeth, are you sure everything is alright?"

"Yes! Stop asking me that!"

"Ok, ok. I found that under your door. So it must have been locked at some point otherwise they'd have left it on your desk." He noticed the dark circles under her eyes, "Did you sleep here all night?"

"No," she lied as she tentatively held the envelope in front of her.

It was sealed this time with a glob of red wax.

Rodney turned to leave; he liked to give people privacy as they opened their mail.

"Stay, Rodney."

He smiled, it could be from John! Maybe it was an apology for hitting on her. A heavy thud hit his stomach-what if it was his letter of resignation.

Weir's face paled as she read it.

_It must be his resignation... _Mckay thought.

"What is it?"

She slid the note over to him; her voice didn't work because when she opened her mouth nothing came but a crackle.

**Did you sleep well? No? Well plenty of time for that. **

**Don't you wish you had protection now?**

"Who wrote this?"

"I don't know, Mckay...I don't know. But it was the same person who wrote this one."

She let him read the first one.

"You have to tell Major Sheppard."

"Yeah..."

"Weir! Someone is after you!"

"I know. I know. But what can I do? I can't make John follow me around all day."

"You're our leader-yes you can."

"No, I can't. Rodney...I made some mistakes –I..."

"What?"

"Never mind. But I can't ask him that right now, ok? I'm going to call a meeting."

"Ok, but before you do that pick off all that sequence. Where did that come from anyways?"

A look of terror flashed across her face.

"My shirt."

"What?"

"IT CAME FROM A SHIRT IN MY CLOSET. THIS FREAK WAS IN MY ROOM!"


	4. Thoughts

**Chapter 4**

With her scream, Elizabeth didn't need to call a meeting. They came to her. Within a matter of seconds Major Sheppard, Ford, and Tayla were at her door. Weir was happy for their prompt response...It made her feel safe, someone was listening for her.

The scars from the day before were still there, usually John would have come right to her and ripped the letters from her hand and squeeze _her_ hand after whispering in her ear that everything would be okay.

She wished for it. But all he did was frown.

"What's wrong, Doctor Weir?" he asked with a sharp voice that stabbed at her heart.

"These!" McKay answered handing the letters to the Major.

He skimmed them over, frowning and then peppered Elizabeth with questions about how she received these threats. But it was formal...not a drop of feeling in one syllable.

"...And why were you at your office that late?"

She couldn't tell him that she was loosing sleep over him. Or should she? Embarrass herself and admit that she loved him?

"Because I had some paperwork I forgot about."

She couldn't.

"Ok...we'll have to interview the staff...uhhh...Ford, I want you to not be on guard...but walk by here, check on Doctor Weir...at her quarters too."

"Why don't you, Major Sheppard?" Elizabeth asked crossing her fingers.

"I'm busy. And Ford is a hundred percent competent."

Ford beamed. He was like a kid being fed a cookie; John didn't serve out compliments that often. Weir however, nodded, trying to look away...back at the letters...

"We have a mission at 1500 hours. Do you want me to leave Ford, or do you think you'll be ok. Just stay behind locked doors and whatnot."

"I'll be fine. Take Ford."

"Great. Then I think we're done here. I'll get Beckett to see if he can analyze these letters."

Everyone turned to leave.

"Major. Would you stay behind?"

"Yes, Doctor Weir."

The others eyed each other as they filed out.

In a silent agreement, McKay, Ford, and Teyla, pretended to walk off, but came right back to the door to overhear their argument. But his time, the couple spoke in hushed tones and could not be overheard.

"John, I'm really worried."

"We're taking all the necessary precautions."

"I...I don't want you to skip on anything because we're not together anymore."

"So you think I'm that shallow. I know how to do my job, I can separate emotion from my work. Can you?"

"I think so."

"You better."

"I know...I know...I have to face you every day without-without being able to tell you how sorry I am."

"You're apology's accepted Elizabeth."

"Then why are you so cold?"

"Because these army regulation jackets are a piece of crap."

"You know what I mean! I'm not a beggar either. This is the last time I'm going to reach out to you."

"I know what you mean."

And he left.

John left before the others could clear away from the door. But he didn't care.

"Suit up," was all he said as he swept past.

_Who does she think she is? Always embarrassing me...Making my life miserable. Who does she think she is? My team laughs at me, instead of talking my suggestions. They laugh. At me. Not at her. Oooh they should laugh at the red sequence sticking to her hair. I did. Oh I know I did. I liked being in her room...It was like invading her inner world. Violating it. Felt so good. Soon that room will be nothing more than a memorial- people mourning her pitiful life. Doesn't she wish she had protection now? Hahaha...Nothing could protect her from me. Nothing._

__

The mission was surprisingly uneventful. Atlantis was equally surprisingly calm. No letters, no stalkers showed up while the team was gone.

As a tradition, after debriefing, the team went to eat, but Sheppard abandoned them claiming he needed to shower because he smelled worse than the dead pig Rodney was planning on eating.

Sitting down at the table with his tray, McKay was happy to note that his sausage links were as savory as ever-despite John.

"Elizabeth is pregnant!" Teyla burst out.

They stared at her in awe...and it all made sense. Of course they were jumping to conclusions...but it was an uneventful afternoon.

"I asked her and she got very angry with me."

"Denial.." Ford mussed.

"And that's why Sheppard's so mad. I mean, look what it does to them! Our Co and his boss! That's totally against military regulations...moral regulations..."

"I bet they had a one night stand."

They nodded, and shoved forkful of food into their mouths. It was real food day on base, and anything other than powdered eggs and spam was a welcome treat.

John sighed as he sat at the edge of his bed, staring at the wall. He'd never had a broken heart before. It was always him doing the dumping. Sadly, he pulled out a small suede back pouch from under his pillow. With a slight tip, a glittering diamond ring fell into his palm. It was his mother's engagement ring...and her, being ever the romantic, made him take it with him to every base he went to just in case he found _"the one". _ Well, he found her and it only made his world flip upside down.

It was lots of fun sneaking off, or creeping into her room at night to join her....It was fun. But obviously not true love on her part.

He tucked the ring back in the pouch. The plan had been, when she announced their relationship to Atlantis, he would propose. They were going to announce it today in fact.

But the Major was resilient as he shoved the pouch into his secrete compartment that hid all his illegal books. (Take one personal item-HAH! )

_Who knows...Maybe on some other mission I'll hook up with some hot alien...I should visit the mainland more often...Check out some of those Athosians..._

He was cured though. Removing the ring from under his pillow was symbolic. John could get over her, move on, and do his job. Atlantis needed him. He needed Atlantis.


	5. Tailgating

**Chapter 5**

McKay was almost through with his meal, and that's saying something as he had 3 portions, when Weir joined them.

As usual, because of the recent events, her face looked pained.

But worse so now.

She sat down as she handed McKay a red envelope.

"What's this?"

One glance at her wince and he knew.

"Read it out loud," Teyla requested.

"Why do you always turn me down? Why do you always embarrass me? Why do you make people laugh at me? It's my turn now. I laugh at you. It's my turn now to see your face all red from blood rushing to it. I would be a much better leader than you, I'm simply way smarter than you. Can't you see that? You blind ignorant diplomat."

A pall of silence swept over the table only to be interrupted by Weir's haunted whisper, "I think it's John...After what I've done to him...I think it's him," her hand clapped over her mouth, "I'm sorry, I'm feeling so nauseated with all this."

The other nodded in unison-she was pregnant.

"It couldn't be the Major. No way," Ford said, ignoring the evidence.

"I know...but we've all seen him fight. He turns into some sort of animal-maybe I turned him into that."

"What did you do?"

She smiled weakly, and then nodded her head. This was time, she supposed to spill her secrete. Her safety, after all was more important than her pride. The crew's safety was more important. If John was sending these letters, he was a threat to everyone.

"You were right in wondering about us-me and John- hugging. You caught us. For the first time. We were always so careful."

"You two have been going out? For how long?"

"A year and a half. We were supposed to tell everyone today. On the anniversary of the day we told each other how we felt. And a day before...What do I do? I deny everything and chicken out. We broke up."

They had finally declared their love for one another when he survived the leach bug. She had visited the infirmary every night. Every night they whispered to each other, conspiring to keep their secrete. Weir told them this much.

"It can't be John, can it?" Elizabeth realized, "No. It can't."

"You should confront him with this," Teyla suggested, "The Major is big on truth."

"You are right. I'm going to go see him."

"Umm...Elizabeth," Rodney said, "Why don't you take someone just in case...he-ah-he..." 

"I understand Rodney. Good thinking. Why don't you come with me?"

"I,ah, actually meant you take Ford."

"Of course you did."

The Major was uncharacteristically unshaven as he answered the door. He was also only wearing a pair of pj bottoms. Elizabeth's eyes fallowed the swells of lean muscles on his arms and chest, but quickly snapped back to focus.

He noticed. But he wasn't amused, and threw on a robe.

"Come in."

"We'd actually rather stay outside, sir."

"Oh? It's not that messy."

"That's not it, sir."

"_Ford_, what's going on? Did someone let a rat loose in my room again?"

"No..."

"John," Elizabeth stepped in, "Are you mad at me for...for not admitting that I loved you?"

His eyes darted to Ford.

"I already told them."

"Oh. That's news. You wouldn't tell anyone before. But I might want to add it's a bit too late."

"I told them because I'm worried you wrote the threats."

For once the Major could say nothing. He stared into Elizabeth's eyes, letting her see the pain. She instantly regretted telling him. He couldn't have written anything that would ever harm her.

"You think that do you?"

"Yes."

"Okay. _Okay_..."

"Is that it?"

He looked back at her with fire in his eyes.

"You think I want to kill you because you embarrassed me? You think I wrote those letters? Elizabeth, do you even know me anymore?!"

"I don't."

"I don't want you to," he looks at Ford, "Come to take me to the Brig and name me Stan?"

"No sir. Not unless Doctor Weir says to."

"Ooh good to know. But I think it's a little late to try and get on her good side."

"John..."

"What do you want me to do? Walk down to the brig myself? Write a letter of resignation? Because you seem to think I write a lot of letters."

"Did you write those threats?"

"No."

"Then who did?"

"If I knew, do you think I'd be putting up with this conversation, Doctor Weir?"

"I'm going to suspend gate travel and..."

"And you're going to have to promote Ford, because I'm handing in my resignation letter."

"What!? I didn't ask you to."

"I'd rather do it on my own than be asked."

"What, John, no, you're the one who can fly those puddle jumpers long distances. You have the Ancient gene!"

"I'll think I'll retire on those breakers in the mainland. Catch up on surfing. Grill hot dogs."

"I just had to ask if you wrote them."

"Aiden, come out for some Athosian beer and football once in a while, hmm? I'm gunna pitch myself a tent...a tax-free year around tail gate party. This isn't so bad."

"Umm...sure sir."

"It's John now. And it's not an obligation."

"John," Elizabeth began.

"Mr. Sheppard to you ma'am," then he shrugged, "Or Major. Some retired people keep their titles."

"Sheppard! I'm sorry if I insulted you. But there's a lot of evidence pointing to that you _did_ write those letters. It mentioned being embarrassed, that you though you were smarter and a better leader..."

"Have I ever said those things to you before? I don't even think them! Now I do though. If I was in charge, I'd examine every piece of evidence before attacking an officer. That's right. I'm glad I'm leaving. Now everyone thinks I'm unhinged and if people doubt my judgment I'm useless. You'll find my letter on your desk soon enough. 'Pleasure working with you."

With that he slammed the door in their faces.

John left his room with his duffle bag slung around his shoulder. Self-imposed exile. But seriously, he was two steps away from the Brig. Weir approaching him first was a nicety. And he knew it was only temporary-till they caught who ever was threatening her. Then they'd come back with floods of apologies...and he'd come back from a nice long-much needed-vacation.

Yes, he was worried about her. But no one on Atlantis was really that crazy to carry anything through. Besides, he really did have 100 confidence in Ford. And it's not like anyone would let him protect her now.

As he walked through the halls, people gave him strange looks and scooted aside. They stopped talking as he walked by and stared with their mouths agape.

"How could he do that?"

"Always knew something was wrong with him..."

"It's the hair..."

"Too bad, he was kinda cute."

"Murder, Weir, whodda though."

He finished walking through the gauntlet and entered the jumper bay.

If he was accused of committing one crime...might as well commit a real one.

Grand theft auto...well...Grand theft.

He smiled at the puddle jumper ahead of him, the one they used for missions. It had food, medical supplies, and an assortment of weapons.

_Alriiight._

Stackhouse ran in into Weir's office; he stood gasping for breath before he could speak.

"Doctor...Doctor Weir...A puddle Jumper's gone...Major took it. Major Sheppard."

"He left?"

"He stole the craft! I have a team ready to come and bring him back."

She threw her head back and laughed.

"John's the best Pilot here. You couldn't catch up to him, or force him to land. Just let him go. Save our fuel."

"Yes, ma'am."

_Just let him go...He's gone. He doesn't love me...And I don't love him._

"Ma'am?"

"Hmm?"

"Did Major Sheppard really threaten you?"

"I'm afraid all the evidence points to it. And...and if he shows up...back on Atlantis...I give who ever full permission to put him in the brig."

_How's that for separating emotion from the job?_


	6. Blood corrected btw

**a/n sorry for such a short chapter! But hey, it's the wkend...And thanks for the correction on the chapters!!!!!**

**Chapter 6**

Three days later...three days without John...three days without any threats.

_It can't be him!_

But Weir sighed and trudged through the rest of the paper work on her desk. She had done her job...and now it was time to move on.

Beckett had his hands full that morning. A crew of scientists had gotten injured from and exploding personal shield.

_What on earth were they trying to do?_

He applied a jellied gauze on Zelenka's burn.

"So, where's McKay? Usually he's with you all. Complaining the loudest."

"Don't know where...I haven't seen him in a while actually."

"Hmm...I bet he's just weary of these personal shield devices."

"Yeah."

Beckett released him and moved on to his next burn victim. Kavenah. Ugh.

"Morning, Kavenah."

"Hmm."

"So were you in charge of this little project?"

"It's not like I'd knew it would explode!"

"Of course not...of course not."

Beckett studied the burn. Blisters and dry scaling...red patches up and down his arm...

"Let me go get something a little stronger than Neosporin."

The doctor scurried off and Kavenah watched him as he disappeared into another room. The scientist slid of the bed, wincing as his bad arm quaked under his weight, and then tiptoed off.

In the storage room, Kavenah's eyes scanned up and down the shelves...till they landed on something that made his eyes flicker with malice. A vial of blood, labeled "Elizabeth Weir Control Sample."

Elizabeth sat at the head of the conference table. She had called a meeting of her senior staff to discuss future operations on Atlantis.

"Where's McKay?"

Her team shrugged, they had hardly noticed, their eyes were on John's empty seat.

"Ford, go check his lab and the mess hall. Teyla-his quarters. We can't have this meeting without him."

Fifteen minutes later they reported back with a similar conclusion: McKay wasn't anywhere to be found.

"I heard a bunch of scientists got hurt in the lab today, maybe he's in the infirmary," Ford said.

"Alright," Elizabeth said as she picked up her communication device, "Is Beckett in? Uh-huh...ok...Is Rodney Mckay one of the scientists? Alright. Thank you."

Her face paled as she hung up.

"What is it?"

"No one has seen Mckay...or Beckett for that matter."

2


	7. John's letter

**Ch7**

a/n Tests and more tests! ARG! Sorry for the short chapters and the long waiting periods!

A thorough sweep of the building confirmed that McKay and Beckett had indeed disappeared. Weir rang the high alert alarms, and armed officers flooded the hallways.

_I wish John was here._

Elizabeth nodded at Ford as she passed him, heading toward her office.

"Wait! Doctor Weir!" He called out.

"Yes?"

He handed her a crisp piece of white paper.

"I went by the Major's to see if he was really gone...You, know I can hardly believe this whole thing...But it's his resignation."

Wearily, Weir read it.

_**Ok...So, I'm outta here...Prbly hitting the breakers as you read this. This isn't really a resignation letter-it's an alert me once I'm off death row type of thing. And if ANYTHING happens, let me know, ok? You know where to find me. I'm bunking with Jinto's crowd. I imagine they'll keep me busy for a while...But I will get bored soon...Ya' know, when not getting shot at for a while, life gets dull. So be safe. Be armed to the teeth. And lock your door Weir, ok? Stick with Ford-Yeah I trust him. I'll end it here because the security detail is approaching and I-ah- "gotta run". –John**_

_**PS. I'm enjoying the puddle jumper-thanks for the company car.**_

Despite their predicament, she smiled and Ford joined in with the laughter.

But their laughter was cut short as she opened her office door.

"Get John back," She whispered coarsely.

1


	8. Et tu Brutus?

**Chapter 8**

Before Ford could carry out her order, he half dragged Elizabeth to the infirmary. He sat her down and turned to a nurse.

"Watch her, she looks pale."

"Ford, I'm fine. Really."

"Watch her."

"Yessir."

Aiden ran for Teyla, and nearly bumped into her as he rounded the corner.

"What is it; you're breathless."

"Come see."

He guided her to Elizabeth's office and swung open the door.

She gasped.

Blood stained her desk in splashy puddles, and the part that didn't stick dripped to the floor, creating red little trails down the table legs.

Teyla walked in, but her boots peeled off the floor, as the blood tried to cling to her and the tiles.

"We should get it tested," she ran her finger along the table and brought the red liquid up to her eyes, "It looks real."

Teyla ran to the infirmary and told the nurse to go gather samples.

Weir was sitting up in a hard plastic chair sipping on water and nibbling at a sugar cookie.

"You okay, Doctor Weir?"

"Yes, I'll be up soon. Don't worry."

"We have everything under control. Ford went to go get Major Sheppard."

"I hope he comes..."

"He will."

Weir looked at her with a forlorn smile and nodded.

"I'm going to go help the nurse clean your desk. Sit tight, ok?"

"That's all I'm good for at the moment."

Teyla smiled and left. As if he was watching, Kavenah entered as soon as Teyla left. He sat himself down next to Elizabeth.

"How you doing?"

"Better. Thanks for asking."

He smiled, and then whispered something into her ear. Her eyes widened and he clamped his unburned hand over her mouth as she tried to scream.

"Oooh Elizabeth," he whispered again, "I am so much smarter than you."

John laid himself out on a make-shift beach towel, and let his pale skin soak up the sun rays. Next to him, Jinto copied the Major, and was equally sprawled out. When John took a sip of water, Jinto quickly followed, and when the Major slid on sunshades, Jinto slid on his. They were actually John's extra set and they fell off the child's face as they were too big and slid down his nose.

To anyone else, it would seem like the perfect stolen moment of the afternoon. For Jinto, it must have been. But, to the Major, all he could revel in was the events of the past couple of days. It still stung that everyone thought he could actually threaten Elizabeth. Worse however, was the realization that he had once again run from a problem. He had run from a court marshal to work in Antarctica, and now he had run from the brig to settle on the mainland. The Major let out a long sigh, and Jinto did the same.

"Major Sheppard, Major Sheppard!"

"What, Jinto?"

"Tell me another story."

"Ok, alright," he sat up, "Once upon a time, lived the handsomest pilot. He could fly anything that had wings. One day, he soared to a great ice continent where all the fair maidens eagerly awaited his arrival. Only, he only cared for one. They called her the one with the red hair. No one had ever been able to win fair lady's heart. But the pilot was lucky, he had charms and wit galore..."

Teyla and the nurse stared down at the centrifuge, and then back at the chart.

"I can not believe it."

"I can't either."

"It is Doctor Weir's blood. But how?"

Before the nurse could answer, Teyla ripped out a loud yawn, and she quickly followed.

"Whaaa...wahht's that hisss?"

Both turned toward the door, and saw a can puffing out clouds.

"Nooo!" Teyla screamed with her last ounce of energy as she lunged at the door.

But it was locked.

Ford strapped himself into the puddle jumper's pilot seat. It was odd without Sheppard next to him. He tried to start the engine, and there was nothing. In his moment of panic, he realized that he didn't have the ancient gene. And everyone with it was gone. There was no way to reach Sheppard. Everything rested on him. Ford drew in a breath and gathered himself together. He'd be ok...they'd be ok.

He reached to unlock the ship's door, but as he looked through the windshield, he saw the scientist's face gleaming madly.

Not panicking, but not being necessarily calm either, Aiden tore at the lock and banged at the door, but it wouldn't unlock.

"Come on! Come on already!"

But nothing would "come on."

He reached for the radio, but nothing worked because he didn't have the ancient gene. Sadly he watched as the scientist opened a can...and let gas seep through the air.

"And the dashing pilot quickly wooed her," John smiled, even as bile rose in his throat at the thought of leaving Weir alone to deal with her stalker, "But then he left, right as things became troublesome and he and his fair lady were threatened. Basically he was a jerk who was too concerned about keeping his hair looking great that-"

"You skipped some of the story!"

"Yeah, well, that's because the end isn't written yet. There's still time."

With that, he got up and ran toward the Puddle Jumper.

Elizabeth opened her eyes, at first everything was black, she blinked again, and the world came into view. She tried to move her hand, but quickly found that was bounded to a chair as well her legs.

Looking up she frowned.

"Rodney? You, too?"

4


	9. You

**Chapter 9**

Rodney managed to smile back at her, but that's all he could do, as he was also tied to a chair. Next to him was an equally bounded Beckett.

"You're up. Good morning."

Elizabeth watched as Kavanah stepped from the shadows and into the light before her. There wasn't much light, the room looked like a box with no entrance, and no exit.

"Have a nice sleep?"

"What are you doing with us?"

"I'm glad you asked, actually. Very glad. See, it seems some time ago I asked you about testing a shield device, and you said no. Some time ago I asked you about another project, and you said no. You always say no, you always ALWAYS ridicule me in front of others. Well no more. No more."

"If your problem's with me then let the others go."

"I can't believe you made John run away. You thought it was him? That's laughable. He isn't clever enough to string more than two sentences together."

"Why don't you let us go?" Elizabeth asked, keeping her resolve.

"Because they have the ancient gene. I want to activate that shield, hook it up to a power source, and amplify it!! I want to do one of MY experiments."

"I don't have the gene."

"No. But you have John Sheppard."

"Like you said, I sent him away."

Kavenah threw his head back and laughed.

"Yes, yes, I thought you had ruined my plan. But you didn't. I know he'll come back. The sooner the better for all of us I dare say."

With ease, John landed the craft in the hanger and just before he began to pop the hatch, he stopped to hear a slight "thump. Thump."

Morse Code. Thump-bump-bump...Sleeping gas...in...hangar...bu-bump-thump...

John nodded and scanned the bay, sure enough there was Ford rapping on the dash board of one of the ships.

_Tried to come get me._

John thought hard for a moment, and two gas masks popped out the roof. Securing one over his face, he rushed to Ford and made sure his second in command was also properly geared.

"Thanks sir."

"Where's Wier?"

"In the infirmary resting. Last I know of at least."

"Let's go," John broke into a sprint and the Lieutenant quickly followed.

Of course she wasn't in the infirmary.

"That's where I left her, sir."

John took off his mask, and Ford did the same, briefly reminding him of Jinto.

"Teyla, Rodney, Beckett?"

"Rodney and Beckett are missing, and Teyla was in Weir's office."

"Ten hut then. Let's find Teyla."

John kept his mask of calmness up, but inwardly he was screaming. It really was some mad man on the loose, and he, the head of security had done nothing.

"Sir...about the whole blaming you thing..."

"Let's find Teyla," John interrupted, not comfortable with long drawn apologies. The boy did his job.

Ford smiled, equally relieved.

Once they reached Weir's office, they saw the womens' slumped bodies.

"Gas mask on."

John tried the door, but it was locked, and a piece of plastic seemed to have been wedged in as well, making a civilized entrance impossible. With a running start, he barreled through the door.

"I can't leave you all for second can I? Everything just gets outta control. Take them to the infirmary, I'll start looking for Doctor Weir and..." John stopped speaking as he eyed the bloody desk, "Fooord."

"Oh, sir, that was a threat, it isn't like the blood from a bludgeoning or anything."

"Thank you. Let's move out."

Ford lifted up Teyla's limp figure and hauled her off towards the infirmary-he'd come back for the nurse in a minute.

Sheppard split away, and walked to where ever his feet would take him. Every door he passed, he opened, every hallway he saw, he searched.

"Doctor Weir! Come on this isn't funny."

He jerked his gun up at the sound of running footsteps and the breathless pants of someone in bad physical condition.

"Hello?"

"Major! Major! I thought you left."

"I did, Kavenah, but I came back."

"Sir, sir, I saw Doctor Weir. She doesn't look good."

With out even needing a nod from the Major, Kavanah led the way.

"Inside here," Kavanah said as he pressed open a seemingly seamless door and walked in.

John didn't even think to ask how the scientist found the place, he was just too grateful to him for leading him to Elizabeth.

He opened his mouth to thank him, but fell short as his eyes landed on Weir. She was strapped to the back of a chair, and across from her was Rodney and Beckett in the same predicament. John drew his gun, and watched for an intruder.

"John! Get out of here!" Elizabeth screamed before Kavanah slapped a hand over her mouth.

"What? Kav..." he stopped speaking as the mad scientist placed a cold silver blade at Elizabeth's neck.

John felt sick to his stomach that he let himself walk into this trap, and equally queasy over seeing his dear friends strapped to chairs with rope that drew blood as it chafted their skin. But, even though it was a trap, he'd never would have found her-them- without being led here.

"Ok, Kavenah. What do you want?"

"You."

4


	10. Catch 21

**Ch.10**

**A/n sorry for the long-time-no-update! But life is sooo busy...**

John slowly drew in the scene once more. Kavanah held all the cards.

"Drop your gun or, how do they say it? 'She gets it'."

"Now what do you want with me? Because you know, there some things I don't mind like going to a football game, but if you want to play house I think you already have enough people."

"Har. Har, Major. The gun-now."

Shrugging, John triggered the safety catch and dropped his weapon on the floor.

"Now kick it to me."

"John, NO! He'll kill us!" Elizabeth shouted.

"You know, Big K, she's right. How about let them go, and I'll stay since I'm the one you needed."

"John, he'll kill _you_."

John heeded the warning mentally, but nothing registered on his face as his big goofy grin remained.

"Let them go and I'm yours. Then I'll kick the gun over."

"Fine."

Kavanah cut the ropes off Weir and then faced the Major again with a smirk. Weir scurried to untie the others.

"How many years did it take you to grow that pony tale?"

"_What_?"

"How-many"

"I heard you Sheppard."

Weir pushed McKay and Beckett out the door, but Kavanah grabbed her by the arm and threw her inside once again.

"Big K, your promise?"

"Thought of something better. Elizabeth, go get the gun for me."

Her desperate eyes met John's and he nodded at her.

"Yeah, yeah, get the gun for him. Dude you have watched Die Hard one too many times."

Elizabeth walked slowly to John and picked up the gun.

"John..."she whispered.

"Get back here."

Elizabeth obeyed and handed the scientist John's only weapon, she handed him their only hope.

"Now, look, I'm up for anything as long as Lizzy's going to be ok. But now that you broke your promise..."

Kavenah drew the blade up to her throat again, scratching off a bit more flesh.

"Wait, what am I doing?" the scientist said as he dropped the knife and aimed the gun at her head, "Now, John, go sit in that chair and let me hook you up."

"Whaat?"

"SIT"

"Roll over!"

Kavenah's finger tightened on the trigger and John sat.

"Elizabeth, take the personal shield and stick it on him, and plug that wire into the socket."

As she follows his instructions with shaking hands, Kavanah continues his self-glorifying speech, "Once you are hooked up, you're ancient gene will activate the shield and that energy will flow to the alternate power source, charging it. We can store it and then power the base's shield. Only, it's going to take a lot out of you, Sheppard. And the shield won't protect you because its energy is being transported."

"It's going to take so much out of you that it will kill you," Elizabeth said as she walked towards the plug.

"I thought I was getting hooked up, here, you know...like a date or something...Not instant death. We went to some _completely_ different high schools."

As they talked Elizabeth plugged the shield into the power source.

"This isn't fun and games."

Kavanah then pulled her in front of John and aimed the gun at her head.

"You're telling me. I'm gunna die."

"That's right you are. Elizabeth, do it, put it on him. NOW!"

"I...I can't. I can't."

"Fine then," With that Kavanah squeezed the trigger.

But the gun didn't fire.

Elizabeth had closed her eyes and was shaking; she let the shield tumble to the floor as she opened her eyes and with sweet relief realized she was alive. She stepped back, towards the door, slowly and quietly so no one would take notice.

"Piece of CRAP!" Kavanah yelled as he dropped to his knees, reaching for the knife, "This'll do its job."

The gun tumbled to the floor.

So the shield, the knife, and the gun lay in a row between John and Kavanah. The Major dove out of his chair and grabbed the gun. Both men laid on the floor, so close they could feel each other's warm, sticky breath. With a wicked smile, Kavanah took the shield and tossed it at the Major so that it stuck to him. Simultaneously, at point blank range, the Major smiled at the click, but then, as the shield hit him, it was as if Muhammad Ali had boxed him good and hard in the stomach, and after deciding that wasn't good enough, clubbing him in the head. As his vision decimated into a dizzy fog, he squeezed out a shot.

"Gun handling 101...release the safety catch," and with that last statement, the Major submitted to the cloud of darkness that was eager to take him away.


	11. reflections

**Ch 11.**

**a/n since I haven't been updating, I figure, hey, 2 chapters is only fair...but heh...I am so cruel...(read and find out) ï**

Weir, who had reached the door, spun around and saw the two bodies on the floor. The scientist was gushing blood, and the other was chalk white and chalk grey all at the same time.

Running, she unplugged the Major and peeled off the shield.

"Please be ok, please!" She pleaded as she bent over him...but he had no pulse...no heart beat.

Instead of wailing, Elizabeth sprung to action and ran to the concealed opening.

_He saved me, I'll save him! _

She swung open the door and called for help, but she didn't need to, Beckett and Rodney, along with Aiden and some reinforcements were jogging down the hall coming at her.

"They're dead!" Elizabeth wept as she sunk down to the floor, "Dead!"

Her resolved melted as she said those words and she realized she had failed him. She had failed him once again. Just as she had when she lied to the others about their relationship.

Aiden and Beckett ran in, and nearly skid on the blood stained floor. Beckett and the medical team went into high gear, yelling, demanding, hauling, but Elizabeth remained in her corner, oblivious to it all.

She had lost her John. Twice.

Elizabeth entered the infirmary and smiled sadly at a bed Labeled "John's" and there was a cup next to it marked the same. It was a gift from all of them because he landed in the infirmary more times that she wanted to count.

But he wasn't there today.

He was downstairs.

1


	12. Downstairs

**Ch.12**

a/n and so it continues...That was an evil cliffy-and I apologize-but it's so much fun...

Weir descended the stairs and a chill shook her body. The farther down she got, the more the urgent tones were heard, and the beeping became more prominent. Oooh, how she held onto the beeping!

They finally got John's heart going with the deliberator and now, she strained her ears to hear every single beep...each one gave her heart a leap of joy.

Finally, she reached their new ICU unit that they placed downstairs, on the lowest level of Atlantis so the patients would have premium privacy.

"How's he doing?" Weir asked from John's bedside as she took hold of his hand and gave it a squeeze.

"Very good actually. We think he'll come to soon. How are _you_ doing Doctor Weir? More nausea or anything?"

"Hmm? No, no I'm fine."

"Why didn't you tell me? You should always tell you doctor-Wait, does John know?" Beckett asked in rapid fire succession.

"Know what?"

"You can't hide it from me, you know...Everyone knows already...the nausea, the mood swings..."

Weir paled.

"You think....you think I'm pregnant?" She laughs, "I'm not, rest assured. Just stress."

Beckett let out a great laugh and told her she better let the rest of the staff know, because they were going to plan a shower soon.

"You're pregnant?"

Elizabeth and Carson glanced back down at the smiling Major. His eyes were still closed, but he was conscious.

"How do you feel?"

"Like jello...jello and spaghetti."

"That shield took a lot out of ya."

"So, is Elizabeth pregnant?"

She shook her head.

"Too bad."

"So you are feeling better," Elizabeth said as she blushed and gave his hand a squeeze.

For a moment, she stared down at him, it was a wonder that he was even alive. He attracted trouble where ever he went, but always seemed to some out ok. Each new experience brought a new sparkle to his eyes.

"John...I'm sorry for, you know, blaming you...and the staff too...everyone...I think we all knew..."

"Liz, it's cool."

She nodded and planted a kiss on his cheek.

"But everything's ok, now, right? Kavanah's dead...but how are Ford and..."

"Everyone's fine. In fact, once you get moved upstairs I think they'll be a party for you."

"Yay. Who's brining the beer?"

Two weeks later, John was able to leave the infirmary for good. As he unpacked his things in his room, he came across the ring.

Once again he sat on his bed and fingered it gently, letting its shine bounce around on the walls.

_I'll ask her tonight._

a/n The end!!!! Yay! I hope you guys enjoyed it. It was sure fun writing. Thank you so much for all the great reviews!!!!

And now role the credits:

Wait...I still own nothing...Nothing at all....Nothing related to the Stargate...at all...

Ok, cancel the credits...

3


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